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Register a new userDeep learning for molecular design - a review of the state of the art
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In the space of only a few years, deep generative modeling has revolutionized how we think of artificial creativity, yielding autonomous systems which produce original images, music, and text. Inspired by these successes, researchers are now applying deep generative modeling techniques to the generation and optimization of molecules - in our review we found 45 papers on the subject published in the past two years. These works point to a future where such systems will be used to generate lead molecules, greatly reducing resources spent downstream synthesizing and characterizing bad leads in the lab. In this review we survey the increasingly complex landscape of models and representation schemes that have been proposed. The four classes of techniques we describe are recursive neural networks, autoencoders, generative adversarial networks, and reinforcement learning. After first discussing some of the mathematical fundamentals of each technique, we draw high level connections and comparisons with other techniques and expose the pros and cons of each. Several important high level themes emerge as a result of this work, including the shift away from the SMILES string representation of molecules towards more sophisticated representations such as graph grammars and 3D representations, the importance of reward function design, the need for better standards for benchmarking and testing, and the benefits of adversarial training and reinforcement learning over maximum likelihood based training.
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Molecular machine learning has been maturing rapidly over the last few years. Improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular properties. However, algorithmic progress has been limited due to the lack of a standard benchmark to compare the efficacy of proposed methods; most new algorithms are benchmarked on different datasets making it challenging to gauge the quality of proposed methods. This work introduces MoleculeNet, a large scale benchmark for molecular machine learning. MoleculeNet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurization and learning algorithms (released as part of the DeepChem open source library). MoleculeNet benchmarks demonstrate that learnable representations are powerful tools for molecular machine learning and broadly offer the best performance. However, this result comes with caveats. Learnable representations still struggle to deal with complex tasks under data scarcity and highly imbalanced classification. For quantum mechanical and biophysical datasets, the use of physics-aware featurizations can be more important than choice of particular learning algorithm.
Nowadays, devices are equipped with advanced sensors with higher processing/computing capabilities. Further, widespread Internet availability enables communication among sensing devices. As a result, vast amounts of data are generated on edge devices to drive Internet-of-Things (IoT), crowdsourcing, and other emerging technologies. The collected extensive data can be pre-processed, scaled, classified, and finally, used for predicting future events using machine learning (ML) methods. In traditional ML approaches, data is sent to and processed in a central server, which encounters communication overhead, processing delay, privacy leakage, and security issues. To overcome these challenges, each client can be trained locally based on its available data and by learning from the global model. This decentralized learning structure is referred to as Federated Learning (FL). However, in large-scale networks, there may be clients with varying computational resource capabilities. This may lead to implementation and scalability challenges for FL techniques. In this paper, we first introduce some recently implemented real-life applications of FL. We then emphasize on the core challenges of implementing the FL algorithms from the perspective of resource limitations (e.g., memory, bandwidth, and energy budget) of client clients. We finally discuss open issues associated with FL and highlight future directions in the FL area concerning resource-constrained devices.
Graphs have been widely used to represent complex data in many applications. Efficient and effective analysis of graphs is important for graph-based applications. However, most graph analysis tasks are combinatorial optimization (CO) problems, which are NP-hard. Recent studies have focused a lot on the potential of using machine learning (ML) to solve graph-based CO problems. Most recent methods follow the two-stage framework. The first stage is graph representation learning, which embeds the graphs into low-dimension vectors. The second stage uses ML to solve the CO problems using the embeddings of the graphs learned in the first stage. The works for the first stage can be classified into two categories, graph embedding (GE) methods and end-to-end (E2E) learning methods. For GE methods, learning graph embedding has its own objective, which may not rely on the CO problems to be solved. The CO problems are solved by independent downstream tasks. For E2E learning methods, the learning of graph embeddings does not have its own objective and is an intermediate step of the learning procedure of solving the CO problems. The works for the second stage can also be classified into two categories, non-autoregressive methods and autoregressive methods. Non-autoregressive methods predict a solution for a CO problem in one shot. A non-autoregressive method predicts a matrix that denotes the probability of each node/edge being a part of a solution of the CO problem. The solution can be computed from the matrix. Autoregressive methods iteratively extend a partial solution step by step. At each step, an autoregressive method predicts a node/edge conditioned to current partial solution, which is used to its extension. In this survey, we provide a thorough overview of recent studies of the graph learning-based CO methods. The survey ends with several remarks on future research directions.
A main driver behind the digitization of industry and society is the belief that data-driven model building and decision making can contribute to higher degrees of automation and more informed decisions. Building such models from data often involves the application of some form of machine learning. Thus, there is an ever growing demand in work force with the necessary skill set to do so. This demand has given rise to a new research topic concerned with fitting machine learning models fully automatically - AutoML. This paper gives an overview of the state of the art in AutoML with a focus on practical applicability in a business context, and provides recent benchmark results on the most important AutoML algorithms.
Multi-task learning (MTL) optimizes several learning tasks simultaneously and leverages their shared information to improve generalization and the prediction of the model for each task. Auxiliary tasks can be added to the main task to ultimately boost the performance. In this paper, we provide a brief review on the recent deep multi-task learning (dMTL) approaches followed by methods on selecting useful auxiliary tasks that can be used in dMTL to improve the performance of the model for the main task.
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